Mammalian cells contain at least four proteolytic systems which appear to serve distinct functions in the turnover of cell proteins. In the cytosol, there is a soluble proteolytic pathway that requires ATP and involves the polypeptide ubiquitin. This multicomponent system catalyzes the selective degradation of highly abnormal proteins and short-lived regulatory proteins. However, this process also appears to be responsible for the breakdown of most proteins in maturing reticulocytes. Boches, F. and A. L. Goldberg, Science, 215:978-980 (1982); Spenser, S. and J. Etlinger, J. Biol. Chem., 257:14122-14127 (1985)) and in growing fibroblasts (Ciechanover, A. et al., Cell, 37:57-66 (1984); Gronostajski, R. et al., J. Biol. Chem., 260:3344-3349 (1985) In cells deprived of insulin or serum, the breakdown of the average cell proteins increases up to 2-fold. This accelerated proteolysis involves the lysosomes, which are also the sites for the breakdown of endocytosed and membrane protein. Another system by which skeletal muscle can increase overall proteolysis involves the Ca.sup.2+ -dependent proteases (calpains I and II). In dystrophic or damaged muscle or in normal muscle after treatments that raise intracellular Ca.sup.+, overall protein breakdown rises, due mainly to activation of the calpains. In addition, there is a nonlysosomal degradative system that functions independently of ATP; in erythrocytes, this system catalyzes the selective breakdown of oxidant-damaged proteins. The relative importance of these systems in the degradation of different cell components under various conditions in muscle is unknown.
In the process requiring Ub, the first step in degradation of many proteins involves their conjugation to this small polypeptide by an ATP-requiring process. The ubiquitinated proteins are then degraded by a 1000-1500 kDa (26S) ATP-dependent proteolytic complex, the Ub-Conjugate-Degrading Enzyme ("UCDEN"). This pathway has been best characterized in reticulocytes, but has also been demonstrated in skeletal muscle and other cells. It is believed to be responsible for the rapid degradation of highly abnormal proteins and many short-lived enzymes or regulatory proteins.
A large (700 kDa) multimeric protease in eukaryotic cells, referred to as the proteasome, is a component of UCDEN. It contains 12-15 distinct subunits and three distinct peptidases of different specificities. By itself, the proteasome is unable to degrade ubiquitinated proteins and provides most of the proteolytic activity of UCDEN.